Category Archives: Archaea

May 16, 2023

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Happy Tuesday! Today’s microbiome digest is microbial ecology heavy, with articles focused on the gut microbiome, Antarctic endoliths’, water microbiomes, and more.

Human gut microbiome

Pathobionts in the tumour microbiota predict survival following resection for colorectal cancer – Alexander et al. – Microbiome

Gut microbiome transitions across generations in different ethnicities in an urban setting—the HELIUS study – van der Vossen et al. – Microbiome

Water and extremophile microbiome

Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability – Ettinger et al. – Microbiome

Genomic insights into cryptic cycles of microbial hydrocarbon production and degradation in contiguous freshwater and marine microbiomes – Vigneron et al. – Microbiome

preprint: Allochthonous groundwater microorganisms affect coastal seawater microbial abundance, activity and diversity – Yanuka-Golub et al. – bioRxiv

Built environment

preprint: Microbial Diversity on Ancestral Halls with Different Visitor Flow Rates Using Amplicon Sequencing – Liu et al. – bioRxiv

Techniques

Comparing genomes recovered from time-series metagenomes using long- and short-read sequencing technologies – Orellana et al. – Microbiome

May 5, 2023

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Today’s microbiome digest is a grab bag that includes ten simple rules for working with other people’s code, an article examining Wolbachia infections in native cockroach populations, and an article examining the role in lactic acid in shaping the human microbiome. Also highlighted is an article focused on human viruses residing within our cells and tissues, which demonstrated a unique virome in nine different human organs through targeted-enrichment viral metagenomics and virus specific qPCRs.

Happy reading!

General microbiome

The structure of prevacuolar compartments in Neurospora crassa as observed with super-resolution microscopy – Bowman – PLOS One

Phylogenetic trees of closely related bacterial species and subspecies based on frequencies of short nucleotide sequences – Nakano et al. – PLOS One

***Unmasking the tissue-resident eukaryotic DNA virome in humans – Pyöriä et al. – Nucleic Acids Research

Predicting partner fitness based on spatial structuring in a light-driven microbial community – Sakkos et al. – PLOS Computational Biology

Multi-site human microbiome

Evaluation of alcohol-free mouthwash for studies of the oral microbiome – Yano et al. – PLOS One

A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome – Zhang et al. – Microbiome

Human gut microbiome

Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the “Lunar Palace 365” experiment – Hao et al. – Microbiome

Animal microbiome

Wolbachia infection in native populations of Blattella germanica and Periplaneta americana – Choubdar et al. – PLOS One

Plant, root, and soil microbiome

Bacterial and fungal community composition and community-level physiological profiles in forest soils – Kunito et al. – PLOS One

Water and extremophile microbiome

Predicting microbial community compositions in wastewater treatment plants using artificial neural networks – Liu et al. – Microbiome

Open ocean and coastal strains of the N2-fixing cyanobacterium UCYN-A have distinct transcriptomes – Muñoz-Marín et al. – PLOS One

Meta-organism gene expression reveals that the impact of nitrate enrichment on coral larvae is mediated by their associated Symbiodiniaceae and prokaryotic assemblages – Tong et al. – Microbiome

Bioinformatics

Ten simple rules for working with other people’s code – Pilgrim et al. – PLOS Computational Biology

Predicting microbe organisms using data of living micro forms of life and hybrid microbes classifier – Raza et al. – PLOS One

iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria – Roux et al. – PLOS Biology

February 25th, 2023

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Bonjour from Paris, France !

In today’s digest you will find a broad range of amazing preprints and published papers! Fontana and collaborator performed a fascinating meta-analysis of publicly datasets obtained from fecal samples of healthy athletes and healthy sedentary adults and revealed the microbiota changes associated with competitive athletes lifestyle.

Today’s non-microbiology pick is an preprint exploring postdoctoral and PhD student’s career self-efficacy in US biological sciences and showed how women and non US citizen have a significant lower level of career self-efficacy compared to their male and US citizen peers. The authors discuss potential causes for these differences and offer recommendations for increasing trainee career self-efficacy.

Have a great Saturday!

Pregnancy and early life

Preprint: Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition – Li et al. – BioRXiv

Human gut microbiome

The human gut microbiome of athletes: metagenomic and metabolic insights – Fontana et al. – Microbiome

Review: Gut microbiome-based strategies for host health and disease – Wang et al. – Critical Reviews in Food Science and Nutrition

The role of diet in shaping human gut microbiota – Rinninella et al. – Best practive & Research clinical Gastroenterology

Preprint: Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria – Robitaille et al. – BioRXiv

Genetic-Phenotype Analysis of Bifidobacterium bifidum and Its Glycoside Hydrolase Gene Distribution at Different Age Groups – Wei et al. – Foods

Animal microbiome

Preprint: Life stage and vaccination shape the gut microbiome of hatchery-reared Atlantic salmon (Salmo salar) – Andres et al. – BioRXiv

Plant, root, and soil microbiome

Preprint: Short- and long-term effects of continuous compost amendment on soil microbiome community – Kraut-Cohen et al. – BioRXiv

Awaking the Dormant Virome in the Rhizosphere – Braga and Schumacher – Molecular ecology

Water and extremophile microbiome

Preprint: A novel order-level lineage of ammonia-oxidizing Thaumarchaeota is widespread in marine and terrestrial environments – Zheng et al. – BioRXiv

Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics – Dart et al. – Viruses

Food microbiology

Analysis of the core bacterial community associated with consumer-ready Eastern oysters (Crassostrea virginica) – Hines et al. – Plos One

Phages and viruses

Review: The Role of Temperate Phages in Bacterial Pathogenicity – Gummalla et al. – Microorganisms

Bioinformatics

Review: Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses – Ibanez-Lligona et al – Viruses

Non microbiology pick

Preprint: Citizenship status and career self-efficacy: An intersectional study of biomedical trainees in the United States – Chatterjee et al. – BioRXiv

December 12, 2022

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Today’s digest has the kind of articles I like best–they are all focused on the unique relationship between microbial communities and their niche environments. These environments span everything from rice seeds to the Mariana Trench to the gut microbiome and even Appalachian coalbeds. Happy reading!


Human gut microbiome

Gut microbiome of helminth-infected indigenous Malaysians is context dependent – Tee et al. – Microbiome

Animal experiments

Taurine metabolism is modulated in Vibrio-infected Penaeus vannamei to shape shrimp antibacterial response and survival – Wang et al. – Microbiome


Plant, root, and soil microbiome

Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome – Mataigne et al. – Microbiome

Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes – Zhang et al. – Microbiome


Water and extremophile microbiome

Comparison of prokaryotes between Mount Everest and the Mariana Trench – Liu et al. – Microbiome


Built environment

Predominance of Methanomicrobiales and diverse hydrocarbon-degrading taxa in the Appalachian coalbed biosphere revealed through metagenomics and genome-resolved metabolisms – Ross et al. – Environmental Microbiology

Evaluation of the Microbial Community and Geochemistry in Produced Waters Collected from CO2 EOR in the Niagaran Pinnacle Reef – Stemple et al. – ACS Earth Space Chem

September 21, 2022

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Human respiratory microbiome

The Microbiota of Human Lung of Pulmonary Tuberculosis and the Alteration Caused by Anti-tuberculosis Drugs – Zhang et al. – Current Microbiology

Human urinary microbiome

Mechanisms of the intestinal and urinary microbiome in kidney stone disease – Miller et al. – Nature Reviews Urology

Human oral microbiome

Comparison of tumor-associated and nontumor-associated esophageal mucosa microbiota in patients with esophageal squamous cell carcinoma – Zhang et al. – Medicine

Human gut microbiome

Differential co-expression networks of the gut microbiota are associated with depression and anxiety treatment resistance among psychiatric inpatients – Thompson et al. – Progress in Neuro-Psychopharmacology and Biological Psychiatry

Early fecal microbiome transfer after donor defecation determines response in patients with moderate to severe ulcerative colitis – Singh et al. – Indian Journal of Gastroenterology

[REVIEW]Modulatory role of gut microbiota in cholesterol and glucose metabolism: Potential implications for atherosclerotic cardiovascular disease Atherosclerosis – Roessler et al. – Atherosclerosis

Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population – Bai et al. – Microbiome

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Metabolic reconstitution of germ-free mice by a gnotobiotic microbiota varies over the circadian cycle – Hoces et al. – PLOS Biology

Inhibitory effects of antibiotic-induced gut microbiota depletion on acute itch behavior in mice – Zhang et al. – Brain Research Bulletin

RhoB affects colitis through modulating cell signaling and intestinal microbiome – Yang et al. – Microbiome

Animal microbiome (for animals in the wild)

Community and shotgun metagenomic analysis of Alligator mississippiensis oral cavity and GI tracts reveal complex ecosystems and potential reservoirs of antibiotic resistance – Perez-Marron et al. – Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology

Microbiome composition is shaped by geography and population structure in the parasitic wasp Asobara japonica, but not in the presence of the endosymbiont Wolbachia – Brinker et al. – Molecular Ecology

Plant, root, and soil microbiome

Mangrove microbial community recovery and their role in early stages of forest recolonization within shrimp ponds – Loiola et al. – Science of The Total Environment

[REVIEW]Current understanding of plant-microbe interaction through the lenses of multi-omics approaches and their benefits in sustainable agriculture – Diwan, Rashid & Vaishnav – Microbiological Research

Mitigating abiotic stress: microbiome engineering for improving agricultural production and environmental sustainability – Phour & Sindhu – Planta

[OPINION]Plant microbiota dysbiosis and the Anna Karenina Principle – Arnault, Money & Vandenkoornhuyse

Food microbiology

Anthocyanin Addition to Kefir: Metagenomic Analysis of Microbial Community Structure – Aydin et al. – Current Microbiology

Metabolic framework of spontaneous and synthetic sourdough metacommunities to reveal microbial players responsible for resilience and performance – Calabrese et al. – Microbiome

July 2, 2022

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Have a nice weekend!

Highlights!

Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides – Miriam N. Ojima – The ISME Journal → this paper contributes to the understanding of the configuration of different bifidobacteria in response to human milk oligosaccharides. 

Genomes of six viruses that infect Asgard archaea from deep-sea sediments – Ian M. Rambo – Nature Microbiology →By using metagenomics, authors describe six relatively large viral genomes, capable to infect members of the Asgard superphylum. The paper remarks on the strange features found in those viral genomes.

TLR4 regulates RORγt+ regulatory T-cell responses and susceptibility to colon inflammation through interaction with Akkermansia muciniphila – Yaojiang Liu – Microbiome → This article demonstrates the existence of “a novel protective role of TLR4 against intestinal inflammation, wherein it can modulate A. muciniphila-associated immune responses”. 

Human and General Microbiome

Review: The microbiome and gut homeostasis – Jee-Yon Lee – Science 

Review: The role of microbiome: a novel insight into urolithiasis – Sen-Yuan Hong – Critical Reviews in Microbiology

Review: Symbiosis: the other cells in development – Tyler J Carrier – Development 

Dysbiosis of the Gut Microbiome Is Associated With Histopathology of Lung Cancer – Xiong Qin – Frontiers in Microbiology

Beneficial Microbes and Compounds

Perspective: Leveraging the Gut Microbiota to Predict Personalized Responses to Dietary, Prebiotic, and Probiotic Interventions – Sean M Gibbons – Advances in Nutrition

Akkermansia muciniphila Alters Gut Microbiota and Immune System to Improve Cardiovascular Diseases in Murine Model – Xin He – Frontiers in Microbiology

Impact of probiotics use on clinical outcomes of immune checkpoint inhibitors therapy in cancer patients – Luying Wan – Cancer Medicine

Review: The gut microbiome as possible mediator of the beneficial effects of very low calorie ketogenic diet on type 2 diabetes and obesity: a narrative review – G Defeudis – Eating and Weight Disorders

Animal Microbiome

The coral pathogen Vibrio coralliilyticus kills non-pathogenic holobiont competitors by triggering prophage induction – Weiquan Wang – Nature Ecology & Evolution

Milk microbiomes of three great ape species vary among host species and over time – Sally L Bornbusch – Scientific Reports

Plant Microbiome

Fungal microbiome shifts on avocado fruit associated with a combination of postharvest chemical and physical interventions – Malick Bill – Journal of Applied Microbiology

Environmental Microbiome

Review: Priorities for ocean microbiome research – the Tara Ocean Foundation – Nature Microbiology

Microbiome Analysis Techniques and Tools

Protocol for correlation analysis of the murine gut microbiome and meta-metabolome using 16S rDNA sequencing and UPLC-MS – Xiaoqing Li – STAR Protocols

microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization – Yang Cao – Bioinformatics

June 29, 2022

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General microbiome

Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station – Urbaniak et al. – Microbiome

Engineering the human gut commensal Bacteroides thetaiotaomicron with synthetic biology – Lai, Hayashi & Lu – Current Opinion in Chemical Biology

Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom – Thomas et al. – Nature Communications

Human oral microbiome

Increase in Bifidobacterium is a characteristic of the difference in the salivary microbiota of pregnant and non-pregnant women – Kato et al. – BMC Oral Health

Human urinary microbiome

Concordance of Urinary Microbiota Detected by 16S rRNA Amplicon Sequencing Versus Expanded Quantitative Urine Culture – Vaughan et al. – American Journal of Obstetrics and Gynecology

Human gut microbiome

Dietary variety relates to gut microbiota diversity and abundance in humans – Huang et al. – European Journal of Nutrition

The gut microbiota composition in patients with right- and left-sided colorectal cancer and after curative colectomy, as analyzed by 16S rRNA gene amplicon sequencing – Suga et al. – BMC Gastroenterology

Long-Term Dietary Effects on Human Gut Microbiota Composition Employing Shotgun Metagenomics Data Analysis – Troci et al. – Molecular Nutrition & Food Research

Functional changes of the gastric bypass microbiota reactivate thermogenic adipose tissue and systemic glucose control via intestinal FXR-TGR5 crosstalk in diet-induced obesity – Münzker et al. – Microbiome

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Perinatal transmission of a probiotic Bifidobacterium strain protects against early life stress-induced mood and gastrointestinal motility disorders – Zhu et al. – Food & Function

Leveraging Existing 16SrRNA Microbial Data to Define a Composite Biomarker for Autism Spectrum Disorder – Xu et al. – Microbiology Spectrum

Animal microbiome (for animals in the wild)

Gut microbiome of century-old snail specimens stable across time in preservation – Chalifour, Elder & Li – Microbiome

Plant, root, and soil microbiome

Soil-derived bacteria endow Camellia weevil with more ability to resist plant chemical defense – Zhang et al. – Microbiome

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

A genome and gene catalog of glacier microbiomes – Liu et al. – Nature Biotechnology

Bioinformatics / Data

Large Scale Genome-Centric Metagenomic Data from the Gut Microbiome of Food-Producing Animals and Humans – Lemos et al. – Scientific Data

Research Note: Choice of microbiota database affects data analysis and interpretation in chicken cecal microbiota – Campos et al. – Poultry Science

[PREPRINT]Predicting metabolomic profiles from microbial composition through neural ordinary differential equations – Wang et al. – bioRxiv

May 6, 2022

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Happy Friday! Today’s microbiome digest is a grab bag of articles on topics such as antibiotic cycling and bacterial contamination in surgery, phage isolated from diseased seafood, and microbial communities in snuff. I was particularly interested to see the article focused on degradation genes found in steel industrial soil communities. Finally, I enjoyed checking out two preprints on oral microbiota in Agta, a group of hunter-gatherers from the Philippines.

General microbiome

Preprint: The making of the oral microbiome in Agta hunter-gatherers – Dobon et al. – bioRxiv

Preprint: Microbial population dynamics decouple nutrient affinity from environmental concentration – Fink et al. – bioRxiv

Beneath the surface: Amino acid variation underlying two decades of dengue virus antigenic dynamics in Bangkok, Thailand – Huang et al. – PLOS Pathogens

Preprint: Hunter-gatherer oral microbiomes are shaped by contact network structure – Muscitto et al. – bioRxiv

Which vaccine attributes foster vaccine uptake? A cross-country conjoint experiment – Stöckli et al. – PLOS ONE

Associations between microbial communities and key chemical constituents in U.S. domestic moist snuff – Tyxobert et al. – PLOS ONE

Multi-site human microbiome

Mycobacterium tuberculosis infection, immune activation, and risk of HIV acquisition – Bender Ignacio et al. – PLOS ONE

The effects of antibiotic cycling and mixing on acquisition of antibiotic resistant bacteria in the ICU: A post-hoc individual patient analysis of a prospective cluster-randomized crossover study – van Duijin et al. – PLOS ONE

Human gut microbiome

Efficacy of laparotomy sponges to reduce bacterial contamination using an in vitro gastrointestinal surgery model – Bezhentseva et al. – PLOS ONE

Animal experiments

Virulence and antimicrobial resistance gene profiles of Staphylococcus aureus associated with clinical mastitis in cattle – Neelam et al. – PLOS ONE

Preexisting Trichinella spiralis infection attenuates the severity of Pseudomonas aeruginosa-induced pneumonia – Rong Long et al. – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Metagenomic analysis for taxonomic and functional potential of Polyaromatic hydrocarbons (PAHs) and Polychlorinated biphenyl (PCB) degrading bacterial communities in steel industrial soil – Sandhu et al. – PLOS ONE

Water and extremophile microbiome

Transcriptomic analysis of chloride tolerance in Leptospirillum ferriphilum DSM 14647 adapted to NaCl – Rivera-Araya et al. – PLOS ONE

Food microbiology

Sole and combined effect of foliar zinc and arbuscular mycorrhizae inoculation on basmati rice growth, productivity and grains nutrient – Mehmood et al. – PLOS ONE

Characterization and complete genome sequence analysis of a newly isolated phage against Vibrio parahaemolyticus from sick shrimp in Qingdao, China – Tian et al. – PLOS ONE

Techniques

Financial incentives to increase stool collection rates for microbiome studies in adult bone marrow transplant patients – Thompson et al. – PLOS ONE

April 8, 2022

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Good morning! Today’s microbiome digest is brought to you by mild insomnia induced by a mid-afternoon coffee. It includes two food related studies, one on pathogenic E. coli found in ready-to-eat foods and the other focused on a antifungal lipopeptide produced by B. velezensis isolated from honey, and an an article focused on a new approach for processing frozen lung and lavage samples for use in microbiome studies. Also included are several articles focused on the gut microbiome, and several preprints focused on soil microbiome studies. Finally, I want to highlight a piece that details the positive outcomes associated with the National Summer Undergraduate Research Project (NSURP). Registration for this year’s program is still open until April 15th, and the organizers are looking for both mentors, mentees, and donors!


Pregnancy and early life

Group B Streptococcus colonization at delivery is associated with maternal peripartum infection – Brigtsen et al. – PLOS ONE

Human gut microbiome

Mycobacterium avium subsp. paratuberculosis and microbiome profile of patients in a referral gastrointestinal diseases centre in the Sudan – Elmagzoub et al. – PLOS ONE

Animal experiments

Vertical transmission of attaching and invasive E. coli from the dam to neonatal mice predisposes to more severe colitis following exposure to a colitic insult later in life – Brand et al. – PLOS ONE

Sex differences in the fecal microbiome and hippocampal glial morphology following diet and antibiotic treatment – Saxena et al. – PLOS ONE

Animal microbiome

Preprint: Anthropogenic disturbance impacts gut microbiome homeostasis in a Malagasy primate – Wasimuddin et al. – bioRxiv

Plant, root, and soil microbiome

Preprint: Microclimate is a strong predictor of the native and invasive plant-associated soil microbiota on San Cristóbal Island, Galápagos archipelago – Schoenborn et al. bioRxiv

Preprint: The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types – Vitamaki et al. – bioRxiv

Preprint: Tracing carbon metabolism with stable isotope metabolomics reveals the legacy of diverse carbon sources in soil – Wilhelm et al. – bioRxiv

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Preprint: Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments – Kohtz et al. – bioRxiv

Food microbiology

Processed ready-to-eat (RTE) foods sold in Yenagoa Nigeria were colonized by diarrheagenic Escherichia coli which constitute a probable hazard to human health – Beshiru et al. – PLOS ONE

Purification and characterization of antifungal lipopeptide produced by Bacillus velezensis isolated from raw honey – Ziong et al. – PLOS ONE

Techniques

An optimized approach for processing of frozen lung and lavage samples for microbiome studies – Wiscovitch-Russo et al. – PLOS ONE

Science, publishing, and career

***National Summer Undergraduate Research Project (NSURP): A Virtual Research Experience to Deliver REAL (Retention, Equity, Access, and Life-Changing) Outcomes for Underrepresented Minorities in STEM – Johnson & Knox – JMBE

January 7, 2022

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Today’s digest covers a range of topics including a duplex qPCR assay to detect lung infections, an investigation into sand fly symbionts, and a characterization of a fermented soybean food (Pe poke). If you want to end the week on a good note, I’d suggest reading the two articles I’ve highlighted below. One demonstrates that flooding and ecological restoration of former cranberry farmland also restores wetland microbial communities and soil function. The second provides a new barcoding strategy for the phenotypic screening of mosquitos that can be applied towards malaria research.

Happy reading!

General microbiome

Controlled spatial organization of bacterial growth reveals key role of cell filamentation preceding Xylella fastidiosa biofilm formation – Anbumani et al. – npj Biofilms and Microbiomes

Bacteria can be selected to help beneficial plasmids spread – Dimitriu et al. – PLOS Biology

Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network – Urchueguía et al. – PLOS Biology

Human respiratory microbiome

Detection of Pneumocystis jirovecii and Toxoplasma gondii in patients with lung infections by a duplex qPCR assay – Wu et al. – PLOS Neglected Tropical Diseases

Animal experiments

***Barcoded Asaia bacteria enable mosquito in vivo screens and identify novel systemic insecticides and inhibitors of malaria transmission – Sturm et al. – PLOS Biology

Molecular phylogeny of heritable symbionts and microbiota diversity analysis in phlebotominae sand flies and Culex nigripalpus from Colombia – Vivero-Gomez – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Shotgun sequence-based metataxonomic and predictive functional profiles of Pe poke, a naturally fermented soybean food of Myanmar – Tamang et al. – PLOS One

***Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland – Rubin et al. – PLOS One

Water and extremophile microbiome

Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment – Remple et al. – npj Biofilms and Microbiomes